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Discovery and Characterization of Cas9 Inhibitors Disseminated across Seven Bacterial Phyla.

Uribe RV, van der Helm E, Misiakou MA, Lee SW, Kol S, Sommer MOA.

Cell Host Microbe. 2019 Nov 13;26(5):702. doi: 10.1016/j.chom.2019.09.005. No abstract available.


Overcoming genetic heterogeneity in industrial fermentations.

Rugbjerg P, Sommer MOA.

Nat Biotechnol. 2019 Aug;37(8):869-876. doi: 10.1038/s41587-019-0171-6. Epub 2019 Jul 8. Review.


Rapid diagnosis of lung infections.

Prodan A, Sommer MOA, Nieuwdorp M.

Nat Biotechnol. 2019 Jul;37(7):725-726. doi: 10.1038/s41587-019-0174-3. No abstract available.


Antibiotic Treatment Drives the Diversification of the Human Gut Resistome.

Li J, Rettedal EA, van der Helm E, Ellabaan M, Panagiotou G, Sommer MOA.

Genomics Proteomics Bioinformatics. 2019 Feb;17(1):39-51. doi: 10.1016/j.gpb.2018.12.003. Epub 2019 Apr 23.


Wiring cell growth to product formation.

Buerger J, Gronenberg LS, Genee HJ, Sommer MOA.

Curr Opin Biotechnol. 2019 Oct;59:85-92. doi: 10.1016/j.copbio.2019.02.014. Epub 2019 Mar 28. Review.


NetSurfP-2.0: Improved prediction of protein structural features by integrated deep learning.

Klausen MS, Jespersen MC, Nielsen H, Jensen KK, Jurtz VI, Sønderby CK, Sommer MOA, Winther O, Nielsen M, Petersen B, Marcatili P.

Proteins. 2019 Jun;87(6):520-527. doi: 10.1002/prot.25674. Epub 2019 Mar 9.


Discovery and Characterization of Cas9 Inhibitors Disseminated across Seven Bacterial Phyla.

Uribe RV, van der Helm E, Misiakou MA, Lee SW, Kol S, Sommer MOA.

Cell Host Microbe. 2019 Feb 13;25(2):233-241.e5. doi: 10.1016/j.chom.2019.01.003. Epub 2019 Feb 5.


Collateral sensitivity constrains resistance evolution of the CTX-M-15 β-lactamase.

Rosenkilde CEH, Munck C, Porse A, Linkevicius M, Andersson DI, Sommer MOA.

Nat Commun. 2019 Feb 6;10(1):618. doi: 10.1038/s41467-019-08529-y.


Publisher Correction: Shared strategies for β-lactam catabolism in the soil microbiome.

Crofts TS, Wang B, Spivak A, Gianoulis TA, Forsberg KJ, Gibson MK, Johnsky LA, Broomall SM, Rosenzweig CN, Skowronski EW, Gibbons HS, Sommer MOA, Dantas G.

Nat Chem Biol. 2019 Feb;15(2):206. doi: 10.1038/s41589-018-0208-z.


Enhanced Metabolite Productivity of Escherichia coli Adapted to Glucose M9 Minimal Medium.

Rugbjerg P, Feist AM, Sommer MOA.

Front Bioeng Biotechnol. 2018 Nov 12;6:166. doi: 10.3389/fbioe.2018.00166. eCollection 2018.


A synthetic medium to simulate sugarcane molasses.

Lino FSO, Basso TO, Sommer MOA.

Biotechnol Biofuels. 2018 Aug 11;11:221. doi: 10.1186/s13068-018-1221-x. eCollection 2018.


The Environmental Exposures and Inner- and Intercity Traffic Flows of the Metro System May Contribute to the Skin Microbiome and Resistome.

Kang K, Ni Y, Li J, Imamovic L, Sarkar C, Kobler MD, Heshiki Y, Zheng T, Kumari S, Wong JCY, Archna A, Wong CWM, Dingle C, Denizen S, Baker DM, Sommer MOA, Webster CJ, Panagiotou G.

Cell Rep. 2018 Jul 31;24(5):1190-1202.e5. doi: 10.1016/j.celrep.2018.06.109.


The evolving interface between synthetic biology and functional metagenomics.

van der Helm E, Genee HJ, Sommer MOA.

Nat Chem Biol. 2018 Aug;14(8):752-759. doi: 10.1038/s41589-018-0100-x. Epub 2018 Jul 16. Review.


Evolution of Antibiotic Resistance in Biofilm and Planktonic Pseudomonas aeruginosa Populations Exposed to Subinhibitory Levels of Ciprofloxacin.

Ahmed MN, Porse A, Sommer MOA, Høiby N, Ciofu O.

Antimicrob Agents Chemother. 2018 Jul 27;62(8). pii: e00320-18. doi: 10.1128/AAC.00320-18. Print 2018 Aug.


Chromosomal barcoding as a tool for multiplexed phenotypic characterization of laboratory evolved lineages.

Jahn LJ, Porse A, Munck C, Simon D, Volkova S, Sommer MOA.

Sci Rep. 2018 May 3;8(1):6961. doi: 10.1038/s41598-018-25201-5.


Shared strategies for β-lactam catabolism in the soil microbiome.

Crofts TS, Wang B, Spivak A, Gianoulis TA, Forsberg KJ, Gibson MK, Johnsky LA, Broomall SM, Rosenzweig CN, Skowronski EW, Gibbons HS, Sommer MOA, Dantas G.

Nat Chem Biol. 2018 Jun;14(6):556-564. doi: 10.1038/s41589-018-0052-1. Epub 2018 Apr 30. Erratum in: Nat Chem Biol. 2019 Feb;15(2):206.


Directed Evolution of Membrane Transport Using Synthetic Selections.

Bali AP, Genee HJ, Sommer MOA.

ACS Synth Biol. 2018 Mar 16;7(3):789-793. doi: 10.1021/acssynbio.7b00407. Epub 2018 Feb 28.


Diverse genetic error modes constrain large-scale bio-based production.

Rugbjerg P, Myling-Petersen N, Porse A, Sarup-Lytzen K, Sommer MOA.

Nat Commun. 2018 Feb 20;9(1):787. doi: 10.1038/s41467-018-03232-w.


Synthetic addiction extends the productive life time of engineered Escherichia coli populations.

Rugbjerg P, Sarup-Lytzen K, Nagy M, Sommer MOA.

Proc Natl Acad Sci U S A. 2018 Mar 6;115(10):2347-2352. doi: 10.1073/pnas.1718622115. Epub 2018 Feb 20.


Biochemical mechanisms determine the functional compatibility of heterologous genes.

Porse A, Schou TS, Munck C, Ellabaan MMH, Sommer MOA.

Nat Commun. 2018 Feb 6;9(1):522. doi: 10.1038/s41467-018-02944-3.


Complete Genome Sequence of Escherichia coli Strain WG5.

Imamovic L, Misiakou MA, van der Helm E, Panagiotou G, Muniesa M, Sommer MOA.

Genome Announc. 2018 Jan 11;6(2). pii: e01403-17. doi: 10.1128/genomeA.01403-17.


Drug-Driven Phenotypic Convergence Supports Rational Treatment Strategies of Chronic Infections.

Imamovic L, Ellabaan MMH, Dantas Machado AM, Citterio L, Wulff T, Molin S, Krogh Johansen H, Sommer MOA.

Cell. 2018 Jan 11;172(1-2):121-134.e14. doi: 10.1016/j.cell.2017.12.012. Epub 2018 Jan 4.


Parts Characterization for Tunable Protein Expression.

Klausen MS, Sommer MOA.

Methods Mol Biol. 2018;1671:3-14. doi: 10.1007/978-1-4939-7295-1_1.


Transfer and Persistence of a Multi-Drug Resistance Plasmid in situ of the Infant Gut Microbiota in the Absence of Antibiotic Treatment.

Gumpert H, Kubicek-Sutherland JZ, Porse A, Karami N, Munck C, Linkevicius M, Adlerberth I, Wold AE, Andersson DI, Sommer MOA.

Front Microbiol. 2017 Sep 26;8:1852. doi: 10.3389/fmicb.2017.01852. eCollection 2017.


Dynamic Rearrangement of Cell States Detected by Systematic Screening of Sequential Anticancer Treatments.

Koplev S, Longden J, Ferkinghoff-Borg J, Blicher Bjerregård M, Cox TR, Erler JT, Pedersen JT, Voellmy F, Sommer MOA, Linding R.

Cell Rep. 2017 Sep 19;20(12):2784-2791. doi: 10.1016/j.celrep.2017.08.095.


Draft Genome Sequences of Three β-Lactam-Catabolizing Soil Proteobacteria.

Crofts TS, Wang B, Spivak A, Gianoulis TA, Forsberg KJ, Gibson MK, Johnsky LA, Broomall SM, Rosenzweig CN, Skowronski EW, Gibbons HS, Sommer MOA, Dantas G.

Genome Announc. 2017 Aug 10;5(32). pii: e00653-17. doi: 10.1128/genomeA.00653-17.


Genetic-Metabolic Coupling for Targeted Metabolic Engineering.

Cardinale S, Tueros FG, Sommer MOA.

Cell Rep. 2017 Aug 1;20(5):1029-1037. doi: 10.1016/j.celrep.2017.07.015.


A versatile one-step CRISPR-Cas9 based approach to plasmid-curing.

Lauritsen I, Porse A, Sommer MOA, Nørholm MHH.

Microb Cell Fact. 2017 Aug 2;16(1):135. doi: 10.1186/s12934-017-0748-z.


Prediction of antibiotic resistance: time for a new preclinical paradigm?

Sommer MOA, Munck C, Toft-Kehler RV, Andersson DI.

Nat Rev Microbiol. 2017 Nov;15(11):689-696. doi: 10.1038/nrmicro.2017.75. Epub 2017 Jul 31. Review.


Assessing glycolytic flux alterations resulting from genetic perturbations in E. coli using a biosensor.

Lehning CE, Siedler S, Ellabaan MMH, Sommer MOA.

Metab Eng. 2017 Jul;42:194-202. doi: 10.1016/j.ymben.2017.07.002. Epub 2017 Jul 12.


Time-Resolved Tracking of Mutations Reveals Diverse Allele Dynamics during Escherichia coli Antimicrobial Adaptive Evolution to Single Drugs and Drug Pairs.

Hickman RA, Munck C, Sommer MOA.

Front Microbiol. 2017 May 24;8:893. doi: 10.3389/fmicb.2017.00893. eCollection 2017.


Dissemination of antibiotic resistance genes from antibiotic producers to pathogens.

Jiang X, Ellabaan MMH, Charusanti P, Munck C, Blin K, Tong Y, Weber T, Sommer MOA, Lee SY.

Nat Commun. 2017 Jun 7;8:15784. doi: 10.1038/ncomms15784.


Adaptive Laboratory Evolution of Antibiotic Resistance Using Different Selection Regimes Lead to Similar Phenotypes and Genotypes.

Jahn LJ, Munck C, Ellabaan MMH, Sommer MOA.

Front Microbiol. 2017 May 11;8:816. doi: 10.3389/fmicb.2017.00816. eCollection 2017.


Development of a Bacterial Biosensor for Rapid Screening of Yeast p-Coumaric Acid Production.

Siedler S, Khatri NK, Zsohár A, Kjærbølling I, Vogt M, Hammar P, Nielsen CF, Marienhagen J, Sommer MOA, Joensson HN.

ACS Synth Biol. 2017 Oct 20;6(10):1860-1869. doi: 10.1021/acssynbio.7b00009. Epub 2017 Jun 21.


Genome Dynamics of Escherichia coli during Antibiotic Treatment: Transfer, Loss, and Persistence of Genetic Elements In situ of the Infant Gut.

Porse A, Gumpert H, Kubicek-Sutherland JZ, Karami N, Adlerberth I, Wold AE, Andersson DI, Sommer MOA.

Front Cell Infect Microbiol. 2017 Apr 12;7:126. doi: 10.3389/fcimb.2017.00126. eCollection 2017.


Rapid resistome mapping using nanopore sequencing.

van der Helm E, Imamovic L, Hashim Ellabaan MM, van Schaik W, Koza A, Sommer MOA.

Nucleic Acids Res. 2017 May 5;45(8):e61. doi: 10.1093/nar/gkw1328.


Sponge Microbiota Are a Reservoir of Functional Antibiotic Resistance Genes.

Versluis D, Rodriguez de Evgrafov M, Sommer MO, Sipkema D, Smidt H, van Passel MW.

Front Microbiol. 2016 Nov 17;7:1848. eCollection 2016.


Transcriptional interactions suggest niche segregation among microorganisms in the human gut.

Plichta DR, Juncker AS, Bertalan M, Rettedal E, Gautier L, Varela E, Manichanh C, Fouqueray C, Levenez F, Nielsen T, Doré J, Machado AM, de Evgrafov MC, Hansen T, Jørgensen T, Bork P, Guarner F, Pedersen O; Metagenomics of the Human Intestinal Tract (MetaHIT) Consortium, Sommer MO, Ehrlich SD, Sicheritz-Pontén T, Brunak S, Nielsen HB.

Nat Microbiol. 2016 Aug 26;1(11):16152. doi: 10.1038/nmicrobiol.2016.152.


Functional mining of transporters using synthetic selections.

Genee HJ, Bali AP, Petersen SD, Siedler S, Bonde MT, Gronenberg LS, Kristensen M, Harrison SJ, Sommer MO.

Nat Chem Biol. 2016 Dec;12(12):1015-1022. doi: 10.1038/nchembio.2189. Epub 2016 Oct 3.


Oral supplementation of healthy adults with 2'-O-fucosyllactose and lacto-N-neotetraose is well tolerated and shifts the intestinal microbiota.

Elison E, Vigsnaes LK, Rindom Krogsgaard L, Rasmussen J, Sørensen N, McConnell B, Hennet T, Sommer MO, Bytzer P.

Br J Nutr. 2016 Oct;116(8):1356-1368. Epub 2016 Oct 10.


Survival and Evolution of a Large Multidrug Resistance Plasmid in New Clinical Bacterial Hosts.

Porse A, Schønning K, Munck C, Sommer MO.

Mol Biol Evol. 2016 Nov;33(11):2860-2873. Epub 2016 Aug 8.


Adaptive responses to cefotaxime treatment in ESBL-producing Escherichia coli and the possible use of significantly regulated pathways as novel secondary targets.

Møller TS, Rau MH, Bonde CS, Sommer MO, Guardabassi L, Olsen JE.

J Antimicrob Chemother. 2016 Sep;71(9):2449-59. doi: 10.1093/jac/dkw198. Epub 2016 Jun 5.


Molecular Buffers Permit Sensitivity Tuning and Inversion of Riboswitch Signals.

Rugbjerg P, Genee HJ, Jensen K, Sarup-Lytzen K, Sommer MO.

ACS Synth Biol. 2016 Jul 15;5(7):632-8. doi: 10.1021/acssynbio.5b00213. Epub 2016 May 3.


RIBOSWITCHES. (Meta-)genome mining for new ribo-regulators.

Sommer MO, Suess B.

Science. 2016 Apr 8;352(6282):144-5. doi: 10.1126/science.aaf6189. No abstract available.


Relation between tetR and tetA expression in tetracycline resistant Escherichia coli.

Møller TS, Overgaard M, Nielsen SS, Bortolaia V, Sommer MO, Guardabassi L, Olsen JE.

BMC Microbiol. 2016 Mar 12;16:39. doi: 10.1186/s12866-016-0649-z.


Simulating Serial-Target Antibacterial Drug Synergies Using Flux Balance Analysis.

Krueger AS, Munck C, Dantas G, Church GM, Galagan J, Lehár J, Sommer MO.

PLoS One. 2016 Jan 28;11(1):e0147651. doi: 10.1371/journal.pone.0147651. eCollection 2016.


CRMAGE: CRISPR Optimized MAGE Recombineering.

Ronda C, Pedersen LE, Sommer MO, Nielsen AT.

Sci Rep. 2016 Jan 22;6:19452. doi: 10.1038/srep19452.


Predictable tuning of protein expression in bacteria.

Bonde MT, Pedersen M, Klausen MS, Jensen SI, Wulff T, Harrison S, Nielsen AT, Herrgård MJ, Sommer MO.

Nat Methods. 2016 Mar;13(3):233-6. doi: 10.1038/nmeth.3727. Epub 2016 Jan 11.


Transient overexpression of DNA adenine methylase enables efficient and mobile genome engineering with reduced off-target effects.

Lennen RM, Nilsson Wallin AI, Pedersen M, Bonde M, Luo H, Herrgård MJ, Sommer MO.

Nucleic Acids Res. 2016 Feb 29;44(4):e36. doi: 10.1093/nar/gkv1090. Epub 2015 Oct 22.


Limited dissemination of the wastewater treatment plant core resistome.

Munck C, Albertsen M, Telke A, Ellabaan M, Nielsen PH, Sommer MOA.

Nat Commun. 2015 Sep 30;6:8452. doi: 10.1038/ncomms9452.

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